Darkness Within
by GoldenSunSheba
Summary: Tormented and tortured for 15 days the Doctor is finally rescued but the events that happened to him is changing him and is scaring Amy and River. Things beging to unfold and for some odd reason he slowly wants to go back...Amy/11 Amy/Rory 11/River
1. Chapter 1

Author's note: Something horrible crossed my mind today and now I'm starting a Fic about it. I warn you this is very dark, there's implied rape, torture and a lot of Angst. Some Spoilers from random bits of Season five not sure when it takes place possibly after the season. I don't Own Doctor who But Steven Moffat needs to stay out of my head.

Darkness Within

Chapter 1

The darkness and silence was actually quiet soothing he hadn't remembered how long he hand been lying on the cold stone floors but he stared at the darkness. How did it all come down to this? No Tardis, no companion…and the unbearable pain he suffered for the last 15 days. The silence would not last but oh he wishes it would. He tries to move but his body aches too much to let him. He knows he's bruised he knows that his ribs are cracked, he knows they'll come back when there ready to torture him some more. He can't scream anymore they barely give him any water and if he wasn't a Time Lord he would most likely be dead already. His eyes where grey now, they lacked color to them and his cloths where tattered torn his rip tweed jacket prevent little cold from hitting his skin. The lack of bow tie and braces made him feel naked all the time. He missed the days he bugged Amy Pond about the bow tie…

Amelia Jessica Pond…where was she now? Was she safe? Had they been captured as well? When the thought of this hit him he felt the warm tear stream down his cheeks. Poor Amy and Rory…they'll never see Leadworth again and it was his fault. The happily married couple would never get to go home…Oh how he was jealous of Rory sometimes. Rory had everything the Doctor could want. He shook his head…no, was fine being who he was…but not now. He closed his eyes the darkness was hurting his eyes he thought back to what had happened…

-Flash Back-

"I always fancied the beach on Cooroliana, perfect spot for a honeymoon; I can get you two a special room!" The Doctor grinned ear to ear at the two of them. Amy had changed recently after their encounter with the Egyptian goddess she really needed a break she smiled over at Rory who's sitting near the stairs.

"As long as there's no running from monsters on this planet," Rory pleaded his blue eyes gazed at Amy who laughed lightly.

"Yeah a little piece and quiet never hurt anyone Doctor," Amy crossed her arms and moved closer to the consol gazing over at him. He beamed at her and nodded.

"I promise no monsters this time," The Doctor raised his hands then the Tardis jolted to one side, "Well that's odd? I'm getting a distress call from the 3rd moon of Cooroliana."

"Guess the honey moon is canceled?" Amy raised her eyebrow Rory sighed and leaned back he was actually looking forward to some alone time with Amy because she gets so close when she's with the Doctor.

"Non sense I'll drop you two off and be back for tea!" He beams.

"Oh no, I'm not letting you go off with the Tardis; it'll be ten years before you come back!" Amy growled at him and he shook his head reassuring her.

"I'll take another form of transportation, no worry I'll leave the Tardis on Cooroliana and take a taxi to the moon," The Doctor flipped a few switches before the Tardis finally landed on the warm beach of Cooroliana. They walked out onto the beach and the twin suns shone making the aqua colored water shimmer. The Hotel dwelled over the beach and all sorts of aliens and even some human laughed and where at the beach relaxing. The sand felt like silk when Amy stepped onto it and she gazed around this had to be the most perfect spot ever, this made up for never going to Reo. There where transport ships and the Doctor pulled out a scanner.

"I'm ready, here you two are, Physic Paper you won all exclusive room with everything you want paid for courtesy the Doctor, that's me," The Doctor pointed out on the Physic paper after handing it to Amy.

"No really?" Amy asked sarcastically and Rory gazed at it over her shoulder.

"Rory Pond…I'll never get use to that," Rory frowned and Amy nudged him lightly.

"Come on we've got dinner and a room to worry about now!"

"I'll meet you back here tomorrow morning!" The Doctor pointed and waved them off making sure he's locked the Tardis, "Oh Amy!"

"What?" She turned back to him and he tossed her the key he was holding. She grinned madly now excited to actually get one. He wouldn't even let Winston touch it for a moment.

"In case you need anything," The Doctor smiled and he walked off the other direction. Rory watched the Doctor and Amy turned to face him.

"Shall we!" she linked her arm with Rory's.

The Doctor fiddled with his sonic screwdriver flipping it open and shutting it. The trip was long and boring and he would have been there sooner if the train didn't get delayed. The distress signal was specifically sent out to him and he had not told Amy or Rory about that. They had specifically requested the Doctor. Gazing at the messaged again it said:

'Help, Doctor, I need your help.'

Maybe it wasn't him but for some odd reason he got the feeling like he was the one that this person needed. After stopping at the 3rd moon the Doctor wondered off no one dared leave the train and looked at him as if he was stark mad getting off here. They seemed to know what was happening and this moon was not a Spa…no by the looks of its icy wall and cold grey stones this looked more like a prison or something of that nature. But the Doctor wasn't willing to back down someone called out for him and he was going to find them. What he was going to find would not be pleasant and the fact they called him they knew already that he was the Last of his kind. Before the Doctor knew it he had been knocked unconscious.

He rubbed the back of his neck as he sat up and gazed around the dark room. His stuff was missing, even his bow tie. All he was wearing now was his trousers and his dress shirt that was slightly dirty from being dragged.

"So you got the distress call," a female voice said, the woman had dark eyes and dark hair she looked human for the most part but she did not act it at all.

"Did you send it?" He asked and she got closer to him gazing into his eyes almost as if she had to make sure he was the real thing. She licked her lips lightly and slammed her fist against his jaw. He flinched he had not expected this welcoming. He reached and rubbed his jaw, "Can't say I'm enjoying my stay here…"

"No you won't ever enjoy it here Time Lord, I've waited too long for you to receive the distress call and you finally gave in. So who was she the girl you brought to the planet?" She grabbed him by the collar and pulled him closer.

"Why does that matter? Who are you?" The Doctor's eyes sharpen that was a foolish move the woman had no tolerance for the Time Lord and slammed him down hard on the floor his head hit the stone and he felt warm blood. He tried to move away but she sat onto of him and grabbed his wrist.

"I wonder who she is. I would love to find her and make her suffer, but then again I have a better plan for you," She leaned down to his ear and whispered, "You stay and be my sex pet…then I leave her alone."

"What if I refuse," The Doctor growled and she smiled pulling out a small syringe she poked it into the Doctor's arm he flinched not expecting that he was still in a daze from her smacking him down as she did. Whatever was in that syringe acted fast the Doctor felt numb.

"You don't have a choice in the matter," She began to undo his trousers and his eyes widened as he tried to move but his body felt like dead wait, "I want you to know my name Doctor I want you to scream it out when I make you come for me," she leaned in and whispered her name and name that haunted him steadily from that moment…

-End of Flash back-

He blinks back tears, course she wasn't the only one…apparently there are others that feel like taking advantage of the young looking floppy haired Time Lord. And what ever she put into him the first time took all his strength. The door opened and the Doctor begged it not to be her and hoped it would be one of the other servants who would just give him some water and leave. But this wasn't so…he flinched as he felt hands brush his cheek. This was gentle…no one was this gentle.

"D-Doctor? Can you hear me?" it was female…it was Scottish.

"A…" that's all that came out his throat ached when he tried to say more and she shushed him and leaned over him. Her read hair drifted around the out line of her face. He could see her green eyes. What did he look like to her? A poor damaged man with no hope left. Amy turned back to the door of his cell.

"River we have to get him out of here," Amy's voice said…River? Ah had she known what happened or had she just been there…he was glad for her finally. She maybe a pain sometimes with her spoilers but she would make sure Amy would be safe. But Rory where was he? Amy wouldn't be safe here…

"I don't think we should move him his ribs are crack and he's in terrible condition," River looked over him and gazed into his eyes she herself had never seen him so in pain and it broke her heart to see him like this. Amy wanted to hug the Doctor and make all the pain disappear and get her old Doctor back but it seemed that he wasn't even there anymore. The Doctor closed his eyes and reached out for Amy's hand with all his strength he took it and in his mind…he said he was sorry…she had to wait for him again…then the Darkness consumed him again.

End of Chapter one

Author's notes: Well that was just dandy wasn't it? Well don't worry I'll try to keep this story updated for all those reading. By the way the pairs vary through the whole story from 11/Amy, Amy/Rory and 11/River.


	2. Chapter 2

Author's notes: Hehehehe I know people are reading even though no comments yet, thanks to those who have favorite the story I hope you enjoy more. Right then onwards, rate M for suggested rape, brutality, torture and blood. I don't own Doctor who but if I did you'd be sure there would be blood in it. Little children need to get immune to the sight of blood…I always hate it when a character gets shot by a bullet or something and they don't bleed. Anyways story…writing…now!

Sheaira: GET ON WITH IT!

Chapter two

-Flash back-

The Doctor groaned what had happened earlier. He couldn't quiet wrap his mind around it his head ached as he sat up and looked around. His memory was hazy but he thinks he knows why he's here again. A prize he was and what a prize…she had been waiting for him for so long, she may look human but she was no human. Nothing innocent about the hooded woman and he tried to remember what happened and why he was in so much pain. He rubbed his hips and realized how sticky his trousers where.

"Yuck…what was I doing?" he murmured to himself he reached for his sonic screwdriver to find nothing. His tweed jacket was on but nothing was in his pockets. He rubbed his jaw it hurt from before when he focused he could remember things clear and this horrified him. He blinked shaking the thought from his mind he had to focus on trying to find a way out of here and back to Amy. He stood and strolled over to the cell door gazing out. There was a scream that startled him a female scream pleading and begging. The Doctor hated this sound some thing was happening to a girl in another cell and he couldn't stop it from happening. He tugged furiously at the door and sighed aggravated. He had to find something anything his head was big enough why couldn't he just thing of a way out. He was clever, cleverest being in the universe. He ran his hand through his hair the screams and pleas didn't help it only brought tears to his eyes.

"STOP IT ALREADY!" he shouted and the silence that fell after was unbearable. He blinked as he stared at the door. The only thing he could imagine was the death of that poor girl. He moaned and backed against the wall. He'd never felt so helpless not even when he was locked in the Pandorica… This was worse, far worse than any nightmare. There where foot steps out side and he raised his head something told him who ever was out there wasn't here to help him.

"She's right you are pretty!" the door opened to reveal a great big man his pants where leather and very revealing which made the Doctor feel sick he wore no shirt and in his hands he held a electric whip. The Doctor shrugged him off and gazed back at his shoes and the man didn't seem to like that and sent the whip straight next to him.

"Ah, pretty boy did you enjoy the girls moans I made her scream for me," he sneered and the Doctor's eyes sharpened.

"You're playing with fire, trust me you really don't ever want to do that again," The Doctor hissed almost threatening. The man chuckled at the Doctor.

"Time Lord, she said you would be hard to break, but you don't look hard to break, skinny, looks like you could break in a heart beat," The whip slaps down and the Doctor grabs it. It burns his hand but his eyes stay deep in anger as he rips the whip away and stand to face this man. The man smiled as the Doctor throws it to the side.

"She said you would fight, you fought even when she had you under the influence of the drug," he smirked, "Bet you don't remember what she did to you."

The Doctor paused, the pain returned to his hips again but he wasn't going to back down from this man no…He was vain with power and that would be the weakness he needed, then he could escape get back to Amy.

"What do you want from me?" The Doctor demanded and the man approached the Doctor did not move he wouldn't coward not now. He clenched his fist ready for anything this man had in mind.

"I want to hear you scream Time Lord oh how I would love to see the mighty Time Lord beg," With one swift motion the Doctor hit the floor the man knocked the wind right out of him with a swift punch to the stomach. He cried out from pain and hit the stone cold ground he hung his head as he pushed himself up. He was yanked by his hair roughly.

"Let us see how long it takes to break you down?" with one hand the man began to unbuckle his leather pants. The Doctor wasn't sure how to react to this and he tried to tug away. No good his grip stay firm but the Doctor wasn't about to give up he'd fight although the pain was unbearable the Doctor tried again to pull himself away using his feet to try and knock the bigger man down, success but it was short lived the Doctor was snagged by the back of the neck and his face hit the stone floor his teeth bit into his tongue and he tasted the blood he flinched in pain. The Bigger man grinned mercilessly and yanked on the Doctor's trousers. Within moment the Doctor's eyes stung with tears again the horrible dirty feeling as the man above him groaned in pleasure…

-End Flash back-

The Doctor's grey eyes opened slowly it was brighter in this room something he wasn't use to and he shut his eyes again. His sides still ached and he wondered where Amy was, why was this place so bright his captors didn't seem to enjoy light so why was this room so bright. Then he felt in the hum of his beloved ship as she tried to sooth his mind, his eyes remained shut as he listened to the Tardis hum softly to him…comforting and haunting at the same time. He prayed that Amy and River where safe…his arms began to ache as he tried to lift them.

"Doctor?" Amy's voice said softly and she gently brushed his bangs with her hand he flinched at her touch and her green eyes looked so sad.

"Don't Amy, there's still a lot of physical damage done to him," Rory's voice said and the Doctor opened his eyes slightly and tried to adjust to the light but he squinted his throat was still dry and his bones ached but he reached and touched Amy's cheek. There was one thing he desperately wanted now.

"Here give him this it might…" Rory turned to her with the glass of cool water and found the Doctor had reached to touch her cheek. What he was letting her see made her wide green doe eyes widen. The nightmare he suffered through he was letting her see and he didn't mean too but she was there and he needed something to hold on to.

-Flashback-

He was naked and she could tell his cloths where tossed near by and he was given was looked like slop in a bowl the Doctor had no appetite after what happened and Amy could understand after all she was in his head seeing what happened. This was only the first day and the Doctor's body was covered in lashes and bruises and he looked horrible his knuckle where bleeding as he continue to pound the stones. He was curled up but Amy could still see the pain.

"Why did they do this to you…Doctor…?" Amy moved closer and tried to touch him but her hands slipped through his body. She was a ghost in this memory and it hurt her more knowing that right now she was sitting at the beach with Rory drink exotic smoothies while her Doctor…her strong lovely Doctor got broken…She remembers watching the third moon and thinking about him wondering what was taking him so long she would have never imagined this would be happening. The screams where heard again from the corridor and the Doctor covered his ears and began to sob uncontrollably. He had snapped and this was only the first day…he would be here for 15 days. 15 days of hell and as the wind howled outside Amy tried to comfort the image as much as she could but what could she say. It grew colder and the Doctor shivered the cage door opened again and Amy stood in front of him but there was just a little girl about 12 years old who was bringing him some water she nearly tripped but got back to her feet the water spilled a bit leaving a trail as she came closer to the Doctor. Her hair was a deep blackish purple and she seemed a lot kinder that the others who had been there. She pushed the water close to him but he did not lift his head to look at her.

"Doctor, who is she?" Amy asked but he didn't reply to her either that or he couldn't reply to her. The girl stood up and hung her head as she left the Doctor.

"I'm sorry…" She closed the door and locked it behind her the screams and pleas died down again. And the silence was the only peace the Doctor got as his eyes stayed open all night the thoughts of what happened haunting him.

-End of Flashback-

Amy flinched as Rory pulled her back the Doctor's hand fell limp against the bed and he stared at the two of them. Tears streamed down her cheek and she looked at Rory.

"Rory, River…do you think she will be alright? The only reason we got back was because she gave me the vortex manipulator to me…but if what happened to the Doctor happens to her…Rory…" Rory gave her a tight comforting hug.

"From what I saw of River I'm sure she'll be back…and we can make the Doctor better…he's tough…" Rory was unsure if they would be able to bring back the Bow tie loving Doctor back. Maybe when all this was done he vowed to go out and find a fez for the Doctor.

"Here give him some water," Rory pushed Amy back lightly and gave Amy the water and she took the glass and was careful. She gently tipped the glass for the Doctor and he drank the cool water it felt great on his dry throat, it numbed the pain for a moment.

"They raped him…"

"Yeah…I kind of figure that," Rory moved away from the two of them. Tears slipped down Amy's cheeks.

"He showed me…it was horrible…" she whispered and the Doctor stared at her with those eyes. Oh she missed how they would light up when he said they would go somewhere new and exciting and now look at him broken into pieces. She regretted not catching on sooner. She just figured the Doctor was doing his Time Lord Things that he needed to do. Not being tortured in such a terrible way. Her thoughts went for River, River had come to tell them that the Doctor was in trouble she had known it way before why couldn't she come sooner. Amy balled her fist up this made the Doctor flinch when he saw her do this.

"No…No I'm sorry…oh god I'm so sorry…" Amy opened her hand again and brushed his hair again. He closed his eyes when she touched him and the Tardis began to sing again a gentle soothing song that put the Doctor to sleep again. Amy hummed with the Tardis and closed her eyes leaning gently next to him making sure she wouldn't hurt him. Her beloved Raggedy Doctor…her imaginary friend…beaten, raped and his pride taken from him. What could she do for him to make this better? How on earth would she fix this?

End of Chapter

Author's notes: Well pretty angst right? Feel free to leave a comment or two I do like to hear feedback. But I know some of you are watching the story and I am glad to hear.


	3. Chapter 3

Author's note: Thank you everyone for bearing with my terrible grammar. Me speak good Englis, but seriously I do hope you are enjoying it no matter how terrible my grammar may be…next thing I know we'll all be thrown into a dessert, kidding!

I do not own Doctor who but if I did I would so write some awesome bad ass stories…and have a better editor…

Sheaira: OI!

Darkness Within

Chapter three

The door to the Tardis opened up and Rory looked over he had been waiting at the Tardis consol pacing wondering and now there she was the curly haired woman. She was holding something her face was grim and she looked up at Rory.

"What happened?"

"They escaped, after all this they ran for it!" she growled harshly and walked up to the consol. The Tardis let out a soft hum and River gazed at her console, "All those years and he never even bothered to tell me until recent," she wasn't angry at him how could she be mad at him.

"What did he say to you when he sent you to us?" Rory went next to her and she pulled out a vial of liquid and placed it into Rory's hand.

"He told me he need you to find him," She said softly and looked at the vial that was in Rory's hand, "You need to give him this, but only very little or he'll go through serious with draw syndromes, the drug they gave to them is very powerful for humans, he's been given more then twice the amount for the last 5 days."

"What did it do to him?" So many questions Rory wanted answered and River shook her head for the first time she really didn't have the answer and this slightly scared Rory and he looked down, "I shouldn't bother them; not yet at least…"

"No let him get as much rest, I believe Amy may be a good healer for him as well. I'll take us out of this place; they won't come searching for us if we aren't near by." River pulled down the leaver and pushed the blue switches removing the breaks and the Tardis silently drifted away from the beach disappearing. The hooded woman glared as the Tardis disappeared. The Man next to her grunted slightly annoyed.

"You just going to let them go?" he hissed, "I enjoyed hearing him scream for you."

"He'll come back to us," she smiled gently, "He'll always want to come back…"

Amy's eyes fluttered open it was colder and she was lying on the floor, she looked around why was the Tardis dark. There was an awful smell of mold and dust it hit her nose and she couldn't help but let out a small sneeze. She lifted herself up it was the same dirty cell she had seen the Doctor in but this felt real. No they couldn't have gotten in the Tardis and taken them. Where was Rory? Wait where was the Doctor? The cell was cold and she wrapped her arms around herself to keep warm. She stood up and looked at the locked door. She pulled out a pin from her hair, she was resourceful she could pick her way out rescue the Doctor then they'd fly out of here and have tea on some tropical planet and her happy bouncy Raggedy Doctor would be better.

The door was harder than she thought to unlock there where foot steps and she pulled out her pin and shoved it back in her hair putting her ear to the door. There where two foot steps one was soft the door clicked and she back up quickly and it swung open the Doctor was pushed inside and she caught him quickly in her arms.

"Doctor, are you alright?" Amy asked when she looked at him he gave her no response until the man with the wipe came into the room again. He grinned down and the Doctor came to life wrapping his arms protectively around Amy.

"I will not let you touch her…" he growled his voice was strained; the man chuckled looking down at the Doctor.

"Like you have any ability to stop me," He grabbed the Doctor by the tweed jacket and threw him against the wall. Amy wouldn't take to this kindly and she stood up.

"You dirty asshole who do you think you are!" she screamed and the man laughed again at her bravery and he snapped the whip down next to her. She flinched but refused to back down or subdue to the jerk who had raped her Raggedy Doctor.

"What have you done with Rory and River!" she demanded.

"What your skinny dumb little husband and the feisty curly blond? HAHAHA! I enjoyed killing the skinny one, he was pathetic." Amy flinched again at this she felt hot tears stream down her cheek had this really happened. No this was impossible.

"Y-You're a lair!" she yelled and the whip snapped across her and she cried out blood streamed down her arm. She heard the Doctor scream out.

"Do what you want to me leave her alone!"

"How sweet he wants to protect you," he gazed down at Amy who held her arm it stung but she wasn't going to give in to this man. She would fight just as the Doctor did but she would be a lot worse. He moved closer to her, she backed up her hazel eyes sharpened and the Doctor struggled to stand to get to his feet to protect Amy. When the man was close enough she gave a kick to fend him off but he grabbed her leg and pushed her against the wall. The Doctor attempt to help her but his body wasn't healed enough and one shove sent him back to the ground.

"I'm going to enjoy this!" he growled slipping one of his hands up her shirt. She screamed loudly struggling.

Amy's eyes snapped opened and she nearly punched Rory out, she stared at him her eyes where wide with fright. Rory nearly jumped off her he had awoken her by shaking her shoulders he had no idea what she was dreaming about and why she was on the floor looking very distressed. She suddenly wrapped her arms tightly around Rory and hugged him tightly.

"I knew he was a lair…" she muttered and Rory blinked.

"Amy, are you alright?" he asked her pushing her back gently, "Why were you on the floor?"

"I'm not quiet sure…wait the Doctor is he alright?" Amy looked back where the Doctor was laying River was over him gazing down at him.

"He's healing alright but I don't think his mind will recover," Rory said to Amy and she stood up and moved around the Doctor gazing at him. He didn't look at all comfortable and she placed a hand on his cheek. His eyes snapped open. There was still the lack of color in them but he smiled at her. A sincere smile, that she was safe and not going to be harmed.

"Amy…" he said and made an attempt to reach for her.

"Shush you are in no shape to talk, I know it's your favorite thing to do," Amy smiled back at him. He nearly laughed at her joke but it hurt too much and she reached for his hand and gave it a squeeze she'd stay right here with him for as long as it took to get him back.

"Amy, there is something I need to talk to you about, in private," River said and the Doctor closed his eyes squeezing her hand slightly tighter.

"I'll be back I promise," she whispered to the Doctor and looked between Rory and River.

"I'll stay with him," Rory said and the Doctor let her hand go weakly. It broke her heart to feel him let go and she followed River just outside the med room.

"Amy, there is a drug they gave to him it cause him to become unconscious of actions he does, it very powerful and if we don't give it to him in small doses he will go through serious withdraw symptoms that will drive him mad," River explained, "When we give him the drug you have to stay away from him all three of us no matter how he pleads for us."

"Why?" Amy asked.

"He might do something he'll regret…Just trust me Amy," River placed a hand on her shoulder. The Tardis rumbled and River looked up, "That is not supposed to happen…Stay here with The Doctor and Rory."

Amy watched River go back to the control room and she gazed back. She closed her eyes trying to rid the thoughts of that man the man who raped her Doctor brutally and had nearly raped her in her dreams…but why would the Doctor's dream be affect her so. She rubbed her arms it was suddenly stinging.

End Chapter

Author's notes: Well not sure where I am going with this one. But I am glad a lot of you are enjoying this. More Torture soon to come and sorry for the delay.


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